De-novo-motif-discovery

What problem does it solve?

This skill identifies novel transcription factor binding motifs in the promoter regions of genes, or directly from genomic regions of interest such as ChIP-seq peaks, ATAC-seq accessible sites, or differentially acessible regions. It employs HOMER (Hypergeometric Optimization of Motif Enrichment) to detect both known and previously uncharacterized sequence motifs enriched within the supplied genomic intervals. Use the skill when you need to uncover sequence motifs enriched or want to know which TFs might regulate the target regions.

Core Features & Use Cases

• De novo motif discovery using HOMER to identify both known and novel transcription factor motifs from genomic regions or promoter gene lists.
• Input flexibility: supports BED, narrowPeak, broadPeak formats or gene lists; outputs organized per project; handles genome assembly specification.
• Standardization guidance and robust outputs: includes chromosome name standardization and well-structured results directories for downstream interpretation.

Quick Start

Provide input genomic regions (BED/narrowPeak/broadPeak) or a gene list and the genome assembly, then run the skill to perform de novo motif discovery with HOMER.